[WIP] lightweight refactoring

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "nsls2ptycho/core/ptycho"]
-	path = nsls2ptycho/core/ptycho
+[submodule "nsls2ptycho/backend/ptycho"]
+	path = nsls2ptycho/backend/ptycho
 	url = ../ptycho.git

MANIFEST.in

@@ -1 +1 @@
-include nsls2ptycho/core/ptycho/*.cubin
+include nsls2ptycho/backend/ptycho/*.cubin

nsls2ptycho/__init__.py

@@ -1,4 +1,6 @@
+import nsls2ptycho.backend
 import nsls2ptycho.core
+import nsls2ptycho.databroker
 import nsls2ptycho.ui
 from ._version import __version__
 

nsls2ptycho/core/__init__.py

@@ -1,2 +1 @@
-import nsls2ptycho.core.ptycho
 import nsls2ptycho.core.widgets

nsls2ptycho/core/utils.py

@@ -11,7 +11,7 @@
 mpi4py.rc.initialize = False
 from mpi4py import MPI
 
-from nsls2ptycho.core.ptycho.utils import split
+from nsls2ptycho.backend.ptycho.utils import split
 
 
 # DEPRECARED: migrated to nsls2ptycho.core.widgets.mplcanvas

nsls2ptycho/core/widgets/mplcanvas.py

@@ -11,7 +11,7 @@
 import numpy as np
 from PIL import Image
 
-from nsls2ptycho.core.ptycho.utils import split
+from nsls2ptycho.backend.ptycho.utils import split
 
 
 def load_image_pil(path):

nsls2ptycho/core/ptycho_recon.py → nsls2ptycho/core/workers.py

@@ -1,16 +1,17 @@
-from PyQt5 import QtCore
 from datetime import datetime
-from nsls2ptycho.core.ptycho_param import Param
 import sys, os
 import pickle     # dump param into disk
 import subprocess # call mpirun from shell
 from fcntl import fcntl, F_GETFL, F_SETFL
 from os import O_NONBLOCK
-import numpy as np
 import traceback
 
-from nsls2ptycho.core.databroker_api import load_metadata, save_data
+import numpy as np
+from PyQt5 import QtCore
+
+from nsls2ptycho.core.ptycho_param import Param
 from nsls2ptycho.core.utils import use_mpi_machinefile, set_flush_early
+from nsls2ptycho.databroker import load_metadata, save_data
 
 
 class PtychoReconWorker(QtCore.QThread):
@@ -81,7 +82,7 @@ def _parse_one_line(self):
 
     def recon_api(self, param:Param, update_fcn=None):
         # "1" is just a placeholder to be overwritten soon
-        mpirun_command = ["mpirun", "-n", "1", "python", "-W", "ignore", "-m","nsls2ptycho.core.ptycho.recon_ptycho_gui"]
+        mpirun_command = ["mpirun", "-n", "1", "python", "-W", "ignore", "-m","nsls2ptycho.backend.ptycho.recon_ptycho_gui"]
 
         if param.mpi_file_path == '':
             if param.gpu_flag:

nsls2ptycho/core/CSX_databroker.py → nsls2ptycho/databroker/CSX_databroker.py

@@ -17,7 +17,7 @@
 
 
 # ***************************** "Public API" *****************************
-# The following functions must exist in nsls2ptycho/core/*_databroker.py,
+# The following functions must exist in nsls2ptycho.databroker,
 # but the function signatures do not need to agree across modules
 # (obviously, it is impossible for all beamlines to have the same setup).
 #   - load_metadata

nsls2ptycho/core/HXN_databroker.py → nsls2ptycho/databroker/HXN_databroker.py

@@ -20,7 +20,7 @@
 
 
 # ***************************** "Public API" *****************************
-# The following functions must exist in nsls2ptycho/core/*_databroker.py,
+# The following functions must exist in nsls2ptycho.databroker,
 # but the function signatures do not need to agree across modules
 # (obviously, it is impossible for all beamlines to have the same setup).
 #   - load_metadata

nsls2ptycho/core/databroker_api.py → nsls2ptycho/databroker/__init__.py

@@ -4,7 +4,7 @@
 
 
 # ***************************** "Public API" *****************************
-# The following functions must exist in nsls2ptycho/core/*_databroker.py,
+# The following functions must exist in nsls2ptycho.databroker,
 # but the function signatures do not need to agree across modules
 # (obviously, it is impossible for all beamlines to have the same setup).
 #   - load_metadata
@@ -22,7 +22,7 @@
 
 
 def _load_HXN():
-    import nsls2ptycho.core.HXN_databroker as hxn_databroker
+    from . import HXN_databroker as hxn_databroker
     global load_metadata, save_data, get_single_image, get_detector_names, db
     load_metadata = hxn_databroker.load_metadata
     save_data = hxn_databroker.save_data
@@ -33,7 +33,7 @@ def _load_HXN():
 
 
 def _load_CSX():
-    import nsls2ptycho.core.CSX_databroker as csx_databroker
+    from . import CSX_databroker as csx_databroker
     global load_metadata, save_data, get_single_image, get_detector_names, db
     load_metadata = csx_databroker.load_metadata
     save_data = csx_databroker.save_data

nsls2ptycho/ptycho_gui.py

@@ -7,15 +7,15 @@
 from nsls2ptycho.ui import ui_ptycho
 from nsls2ptycho.core.utils import clean_shared_memory, get_mpi_num_processes, parse_range
 from nsls2ptycho.core.ptycho_param import Param
-from nsls2ptycho.core.ptycho_recon import PtychoReconWorker, PtychoReconFakeWorker, HardWorker
-from nsls2ptycho.core.ptycho_qt_utils import PtychoStream
+from nsls2ptycho.core.workers import PtychoReconWorker, PtychoReconFakeWorker, HardWorker
+from nsls2ptycho.core.qt_utils import PtychoStream
 from nsls2ptycho.core.widgets.list_widget import ListWidget
 from nsls2ptycho.core.widgets.mplcanvas import load_image_pil
-from nsls2ptycho.core.ptycho.utils import parse_config
+from nsls2ptycho.backend.ptycho.utils import parse_config
 from nsls2ptycho._version import __version__
 
 # databroker related
-from nsls2ptycho.core.databroker_api import db, load_metadata, get_single_image, get_detector_names, beamline_name
+from nsls2ptycho.databroker import db, load_metadata, get_single_image, get_detector_names, beamline_name
 
 from nsls2ptycho.reconStep_gui import ReconStepWindow
 from nsls2ptycho.roi_gui import RoiWindow
@@ -570,7 +570,7 @@ def start(self, batch_mode=False):
             else:
                 self._scan_points[0] *= -1.*self.param.x_direction
                 self._scan_points[1] *= self.param.y_direction
-                # borrowed from nsls2ptycho/core/ptycho_recon.py
+                # borrowed from nsls2ptycho/core/workers.py
                 if self.param.mpi_file_path == '':
                     if self.param.gpu_flag:
                         num_processes = str(len(self.param.gpus))

nsls2ptycho/roi_gui.py

@@ -4,9 +4,9 @@
 
 import numpy as np
 from nsls2ptycho.core.widgets.imgTools import find_outlier_pixels, find_brightest_pixels, rm_outlier_pixels
-from nsls2ptycho.core.ptycho_recon import HardWorker
+from nsls2ptycho.core.workers import HardWorker
 from nsls2ptycho.core.widgets.badpixel_dialog import BadPixelDialog
-from nsls2ptycho.core.databroker_api import save_data
+from nsls2ptycho.databroker import save_data
 
 
 class RoiWindow(QtWidgets.QMainWindow, ui_roi.Ui_MainWindow):

setup.py

@@ -24,12 +24,12 @@
     from glob import glob
     extensions = []
     # this doesn't work because setuptools doesn't support glob pattern...
-    #extensions = [Extension("*", ["nsls2ptycho/core/ptycho/*.c"])]
-    for filename in glob("nsls2ptycho/core/ptycho/*.c"):
+    #extensions = [Extension("*", ["nsls2ptycho/backend/ptycho/*.c"])]
+    for filename in glob("nsls2ptycho/backend/ptycho/*.c"):
         mod = os.path.basename(filename)[:-2]
-        extensions.append(Extension("nsls2ptycho.core.ptycho."+mod, [filename]))
+        extensions.append(Extension("nsls2ptycho.backend.ptycho."+mod, [filename]))
 else:
-    extensions = cythonize("nsls2ptycho/core/ptycho/*.pyx")
+    extensions = cythonize("nsls2ptycho/backend/ptycho/*.pyx")
 
 # see if PyQt5 is already installed --- pip and conda use different names...
 try:
@@ -39,7 +39,7 @@
 
 # for generating .cubin files
 # TODO: add a flag to do this only if GPU support is needed?
-import nsls2ptycho.core.ptycho.build_cuda_source as bcs
+import nsls2ptycho.backend.ptycho.build_cuda_source as bcs
 cubin_path = bcs.compile()
 
 # if GPU support is needed, check if cupy exists
@@ -71,10 +71,16 @@
 setup(name=NAME,
       version=__version__,
       #packages=find_packages(),
-      packages=["nsls2ptycho", "nsls2ptycho.core", "nsls2ptycho.ui", "nsls2ptycho.core.ptycho", "nsls2ptycho.core.widgets"],
+      packages=["nsls2ptycho",
+                "nsls2ptycho.core",
+                "nsls2ptycho.backend",
+                "nsls2ptycho.backend.ptycho",
+                "nsls2ptycho.databroker",
+                "nsls2ptycho.core.widgets",
+                "nsls2ptycho.ui"],
       entry_points={
           'gui_scripts': ['run-ptycho = nsls2ptycho.ptycho_gui:main'],
-          'console_scripts': ['run-ptycho-backend = nsls2ptycho.core.ptycho.recon_ptycho_gui:main']
+          'console_scripts': ['run-ptycho-backend = nsls2ptycho.backend.ptycho.recon_ptycho_gui:main']
       },
       install_requires=REQUIREMENTS,
       #extras_require={'GPU': 'cupy'}, # this will build cupy from source, may not be the best practice!